Main
Patrick Cherry
PhD scientist and professional critical thinker, problem-solver, and science communicator. At the interface of data science, genomics, and statistics; skilled at data visualization, bioinformatics, next-generation sequencing (NGS), and tool-building. I’ve coded reproducible pipelines for high-throughput experimental designs and genomic analyses. I’ve launched best-in-class oncology reference standards and analyzed NGS data from Illumina, MGI, and Element. Originally trained in Molecular Biology, I am passionate about advancing data science and bioinformatics to improve human health and to understand biology.
Education
PhD
University of Colorado School of Medicine
Aurora/Denver, Colorado
May 2019 - Aug 2013
- Ph.D. in Molecular Biology. Advisor: Jay Hesselberth, PhD
- Thesis: RNA terminus chemistry impact decay events that target HAC1 mRNA during the Unfolded Protein Response
BA
Hendrix College
Conway, Arkansas
May 2013 - Aug 2009
- Biochemistry and Molecular Biology, with Distinction. Advisor: Andres Caro, PhD
- Senior Capstone Project showing key stress response gene expression changes to oxidative stress in liver cells
- Minor in Mathematics; PI: Lars Seme; Project: Newton’s method as a fractal chaotic dynamical system
Industry Experience
I currently split my time between wet lab and computational activities. I have worked in a variety of roles ranging from HTP strain onboarding to genomics scientist. I like collaborative environments where I can learn from my peers and in turn teach others.
Senior Scientist, Oncology
BillionToOne
Menlo Park, CA
Current - Sep 2024
- Generated 500+ automated ddPCR primer / probe designs with pipeline in
snakemakeusings3database of variant data andprimer3primer selection - Informed key product decisions with historical analyses using PostgreSQL / ssh and s3 data sources and linear mixed-effects modeling
Senior Scientist, Genomics
Twist Bioscience
South San Francisco, California
Apr 2024 - Jan 2021
- Invented and introduced multiple new products to market, yielding $1M+ in new revenue as Tech Lead, including: Pan-cancer cfDNA (v1 & v2), CNV Controls, RNA Fusion Controls, Fragmentome Controls, RNA-seq, and primer / adapter removal methods for highly-multiplexed dsDNA pools
- Answered biological and business questions with DoE and data analysis using
Rand the libraries:dplyr,dbplyr,DBI,purrr,ggplot2,Bioconductor,DEseq2,seurat,tidymodels,glm,nls,lme4,AlgDesign, and more - Edited and maintained production QC pipelines with automated reporting using
Pythonand the libraries:NumPy,pandas,polars,seaborn,statsmodels,biopython,pybedtools,pysam,vcfpy,scanpy,Jinja2(withCSS),WeasyPrint,and others - Maintained production code (
gitversion control with code review) with CD (github actions); operated in high-performance compute environmentawss3andDatabricksusing Unix shell /bashtools, likessh,STAR-fusion,GATK, BaseSpace CLI,bwa,bedtools,samtools,vcftools,UMI-tools/fgbio; Confluence documentation - Authored internal
Rpackage “twistcolorpal” on Github with help files to help scientists style plots to Twist branding - Answered production and business questions with original
SQLqueries forSnowflake-based database
Scientist I, NGS Core & Strain-Build Process Development
Zymergen, Inc.
Emeryville, California
Jan 2021 - Apr 2019
- Boosted NGS Core genotyping success by 45% using DoE experimentation, data-driven decision-making, and teaching; Guided demanding and diverse internal customers on complex NGS experiments
- Built and disseminated
RmarkdownandJMPstatistical templates for autonomous NGS data exploration - Coded plasmid and strain build and QC experiments using Zymergen’s alembic Python API to LIMS database
- Rendered strain build and plasmid build reports from LIMS
SQLdatabase inMySQLWorkbench
Research Experience
I worked on a few projects during my PhD, and the RNA repair project led me to custom 5′-OH RNA-seq libraries, which inspired my fascination with transcriptomics and bioinformatics.
Doctoral Research
University of Colorado School of Medicine
Aurora/Denver, Colorado
May 2019 - May 2014
- Wrote, revised, & published two academic papers on RNA repair & yeast genetics
- Engineered and characterized genetic bypass of essential genes in budding yeast; on-boarded CRISPR/Cas9 for efficient and precise gene knock-in and scarless knock-out
- Performed RNA-seq analysis with
bowtie2on departmental cluster usingbjobsand visualization in R-Studio server - Optimized custom RNA-seq library protocol; independently planned, executed, troubleshooted RNA modification detection
- Routinely conducted northern blotting, targeted depletion, primer extension, splinted ligation, and other esoteric DNA and RNA experiments
Undergraduate Research Assistant
Lab of Dr. Andres Caro, Hendrix College
Conway, Arkansas
Jan 2013 - Jan 2012
Summer Undergraduate Research Fellowship
Lab of Dr. Michael Shiloh, UT Southwestern Medical Center
Dallas, Texas
Jan 2012 - Jan 2012
Research Assistant
Lab of Dr. Joy Sturtevant, Louisiana Health Sciences Center
New Orleans, Louisiana
Jan 2011 - Jan 2010
Intellectual Property
Working at Twist and Zymergen on new product research requires confidentiality, but public evidence of accomplishments often comes in patent applications. The Legal teams know me well for being a helpful expert in the process.
Methylation-mediated adapter removal on nucleic acid sequences
Twist Bioscience
South San Francisco, California
Mar 2023
- US 63-317,466
Expansion of cfDNA for Libraries
Twist Bioscience
South San Francisco, California
Nov 2021
- US Prov. Pat. Ref No 823.102
Libraries for mutational analysis
Twist Bioscience
South San Francisco, California
Apr 2021
- US Prov. Pat. Ref No 823.101
- Configuration and fabrication of synthetic DNA & RNA reference standards and synthetic variant sequences
Method for counterselection in microorganisms
Zymergen, Inc.
Emeryville, California
Mar 2021
- US 2021_0087586 A1
- Demonstration of novel counterselection mechanism in non-model Bacillus microbe for genetic modification
Selected Publications
I communicate my results clearly, both in writing and in live presentations. I enjoy writing research papers, but my career has required more tech notes and app notes recently.
Twist cfDNA Pan-Cancer Reference Standard v2 Technical Guidance
Twist Bioscience Product Sheet & FAQ
South San Francisco, California
Jan 2024
- Patrick Cherry, Lydia Bonar, & Mike Bocek
Characteristics and specificity of the wild-type / 0% VAF reference material
Twist Bioscience
South San Francisco, California
Apr 2022
- Patrick Cherry & Mike Bocek
Twist Pan-cancer synthetic reference materials technical guide (deprecated)
South San Francisco, California
Dec 2021
- Patrick Cherry & Mike Bocek
Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response
Aurora/Denver, Colorado
Mar 2019
- Cherry, P., Peach, S., & Hesselberth, J.
Genetic bypass of essential RNA repair enzymes in budding yeast
Aurora/Denver, Colorado
Dec 2017
- Cherry, P., White, L., York, K., & Hesselberth, J.
Selected Presentations & Talks
I give audience-centered presentations by adapting on the fly and over time to the venue and occasion. I like to transfer knowledge by giving methods/best practices talks whose slides can also serve as documentation.
Twist pan-cancer reference standard V2: Enhanced precision and reduced errors in ctDNA analysis
Advances in Genome Biology and Technology, Twist Bioscience
Orlando, Florida
Feb 2024
- Lydia Bonar, Patrick Cherry, Michael Bocek, Shawn Gorda, Derek Murphy, and Esteban Toro
High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring
International Society of Liquid Biopsy Annual Congress, Twist Bioscience
Madrid, Spain
Nov 2023
- Tina Han, Tong Liu, Michael Bocek, Patrick Cherry, Shawn Gorda, Nairi Pezeshkian, Dan Nasko, Po-Yuan Tung, Derek Murphy, and Esteban Toro
High sensitivity detection of specific ultra low-frequency somatic mutations for minimal residual disease (MRD) monitoring
American Association for Cancer Researchers, Twist Bioscience
Orlando, Florida
Apr 2023
- Tong Liu, Michael Bocek, Patrick Cherry, Shawn Gorda, Jean Challacombe, Derek Murphy and Esteban Toro
An end-to-end workflow for accurate methylation detection
American Association for Cancer Researchers, Twist Bioscience
Orlando, Florida
Apr 2023
- Lydia Bonar, Kristin Butcher, Michael Bocek, Holly Corbitt, Bryan Hoglund, Cibelle Nassif, Patrick Cherry, Derek Murphy, Jean Challacombe, Esteban Toro
Twist pan-cancer synthetic RNA fusion control for assay development
American Association for Cancer Researchers, Twist Bioscience
Orlando, Florida
Apr 2023
- Patrick Cherry, Jason Corwin, Yu Cai, Kit Fuhrman, Jean Challacombe, Derek Murphy, Esteban Toro
Colorado RNA Club Industry Session
Colorado RNA Club
Boulder, Colorado
Apr 2023
Use of synthetic CNV fragments to mimic copy number alterations for ctDNA reference standards
Advances in Genome Biology and Technology, Twist Bioscience
Hollywood, Florida
Feb 2023
- Jason Corwin, Patrick Cherry, Shawn Gorda, Michael Bocek, Jean Challacombe, Derek Murphy, Esteban Toro
Methylation Controls to detect for methylation level quantification in the Twist Targeted Methylation Sequencing workflow
Advances in Genome Biology and Technology
Hollywood, Florida
Feb 2023
- Kristin Butcher, Michael Bocek, Patrick Cherry, Jean Challacombe, Esteban Toro
Efficient, high sensitivity detection of oncogenic variants with UMIs and target enrichment
European Human Genetics Conference
Vienna, Austria
May 2022
- Michael Bocek, Lydia Bonar, Jean Challacombe, Richard Gantt, Patrick Cherry, Rebecca Liao, Derek Murphy and Esteban Toro
Twist pan-cancer synthetic reference materials for cell-free DNA (cfDNA) assay development
American Association for Cancer Researchers, Twist Bioscience
New Orleans, Louisiana
Apr 2022
Pan-cancer Reference Standard: Methods in Automation & Future Needs
Twist Automation Group Meeting
South San Francisco, CA
Apr 2022
Twist reference material products: current methods and future applications
Twist R&D Symposium
South San Francisco, CA
Mar 2022
Pan-cancer Reference Standard: Methods & Lessons from NPI & QC
Twist R&D Meeting
South San Francisco, CA
Feb 2022
Molecular Methods Meet the Standards: Or how I learned to stop worrying and love UV-quantification
Twist R&D Meeting
South San Francisco, CA
Jul 2021
Colorado RNA Club Industry Session
Colorado RNA Club
Boulder, Colorado
Apr 2021
R use at Zymergen
Z-Tech Talk
Emeryville, CA
Jun 2020
Data-driven troubleshooting of NGS experiments
Data Science Talk
Emeryville, CA
Apr 2020
NGS Sample Preparation Deep-Dive
NGS Technical Talk Series
Emeryville, CA
Mar 2020
RNA terminus chemistry potentiates decay events that target HAC1 mRNA during the unfolded protein response
Thesis Defense Seminar
Aurora, Colorado
Jan 2019
RNA modification and decay regulates the unfolded protein response
Rocky Mountain Yeast Meeting Poster
Fort Collins, Colorado
Jan 2019
What the unfolded protein response teaches us about RNA decay
Bolie Scholar Talk, Molecular Biology Program Retreat
Winter Park, CO
Oct 2018
Genetic bypass of essential yeast RNA repair enzymes
Rocky Mountain Yeast Meeting Poster
Golden, Colorado
Jan 2018
Genetic bypass of essential yeast RNA repair enzymes
Molecular Biology Program Update Talk
Aurora, Colorado
Oct 2017
RNA processing regulates the unfolded protein response
CSHL: mRNA Processing Meeting Talk
Cold Spring Harbor, New York
Aug 2017
Genetic bypass of essential yeast RNA repair enzymes
Rocky Mountain Yeast Meeting Poster
Boulder, Colorado
Jan 2017
RNA processing regulates the unfolded protein response
RNA Club Talk
Boulder, Colorado
Dec 2016
RNA Healing and Destruction
Molecular Biology Program Update Talk
Aurora, Colorado
Oct 2016
RNA processing regulates the unfolded protein response
Rocky Mountain Yeast Meeting Poster
Fort Collins, Colorado
Jan 2016
Turnover of endonucleolytic products of No-Go mRNA decay
RNA Stability Meeting
Estes Park, Colorado
Jun 2015
RNA 5′-kinase-mediated co-translational mRNA decay
Molecular Biology Program Update Talk
Aurora, Colorado
Feb 2015
RNA 5′-kinase-mediated co-translational mRNA decay
Rocky Mountain Yeast Meeting Poster
Aurora, Colorado
Jan 2015
RNA 5′-kinase-mediated co-translational mRNA decay
Rocky Mountain Yeast Meeting Poster
Boulder, Colorado
Jan 2014
Coordinated upregulation of antioxidant protection and mitochondrial DNA biosynthesis in liver cells by oxidative stress
Senior Undergraduate Capstone Research Talk
Conway, Arkansas
Jan 2013
Trainees & Direct Reports
While I’ve not held a role with “manager” in the title, all Scientist positions I’ve accepted have involved formal report management responsibility. I take managing and mentoring seriously; I emphasize trust, learning, and growth with my reports.
Derek Cai, BS, University of California San Diego, Research Associate I
Twist Bioscience
South San Francisco, California
Jan 2024 - Jan 2022
Lydia Bonar, MS, Johns Hopkins University, Scientist
Twist Bioscience
South San Francisco, California
Jan 2024 - Jan 2021
Alonzo Lee, BS, University of California Santa Cruz, Scientist
Twist Bioscience
South San Francisco, California
Jan 2022 - Jan 2021
Kaisle Hill, BA, University of California Berkeley, Senior Research Associate
Zymergen, Inc.
Emeryville, California
Jan 2021 - Jan 2020
Rachel A Jones, MS, University of Arizona, Postdoctoral Fellow
University of Colorado School of Medicine
Aurora/Denver, Colorado
Jan 2017
Laura K White, MS, Biotechnology, Johns Hopkins University, Postdoctoral Fellow
University of Colorado School of Medicine
Aurora/Denver, Colorado
Jan 2016
Haven Himmighoefer, Undergraduate, University of Colorado Denver
University of Colorado School of Medicine
Aurora/Denver, Colorado
Jan 2016 - Jan 2014
Leslie Aranda, Undergraduate, University of California Riverside
University of Colorado School of Medicine
Aurora/Denver, Colorado
Jan 2015